.. _analysis: Analysis ======== In this chapter different ways of analyzing your trajectory are described. The names of the corresponding analysis programs are given. Specific information on the in- and output of these programs can be found in the tool documentation :ref:`here `. The output files are often produced as finished Grace/Xmgr graphs. First, in sec. :ref:`usinggroups`, the group concept in analysis is explained. :ref:`selections` explains a newer concept of dynamic selections, which is currently supported by a few tools. Then, the different analysis tools are presented. .. toctree:: :maxdepth: 2 analysis/using-groups analysis/looking-at-trajectory analysis/general-properties analysis/radial-distribution-function analysis/correlation-function analysis/curve-fitting analysis/mean-square-displacement analysis/bond-angle-dihedral analysis/radius-of-gyration analysis/rmsd analysis/covariance-analysis analysis/dihedral-pca analysis/hydrogen-bonds analysis/protein-related analysis/interface-related